Bug fixes #602
Merged
Bug fixes #602
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This PR fixes some bugs that were introduced recently in #593 #594 and probably others. Some stem form the fact that not all edits were merged (e.g. $wm_file variable was not set, but is going to be set in the edit PR #591 ), then this needs to be changed back. Other were from the fact that brun_fastsurfer does not seem to be updated to the version that would be necessary in order to run things in parallel, so those change have been reverted for now. Other bugs include incorrect linking in talairach-reg.sh and incorrect usage of $sd instead of $SUBJECTS_DIR in recon_surf.sh:
talairach-reg.sh(affects also regular stream)$SUBJECTS_DIRduring -base inrecon-surf.sh(affects longitudinal stream)